GitLab

* Use fixed point spread charge on RDNA4 as it is faster

Even though RDNA4 (gfx12) has global_atomic_add_f32, micro-benchmarks and OpenMM benchmarks show
that it is very slow compared to global_atomic_add_u64.

* Add a workaround for fixed point gridSpreadCharge on RDNA4

Workaround for rare cases when few values of pmeGrid are very large and
incorrect. The cause is unknown. Why this workaround or other irrelevant
changes like printf help is also unknown.

* Add a workaround for infinite loop in computeNonbonded (HIP)

computeNonbonded hangs in some tests (without neighbor list).
Reproducible on ROCm 6.4 and 6.4.1 (maybe on older versions too) on various architectures (both CDNA and RDNA).
Affected tests: TestHipATMForce, TestHipMonteCarloBarostat, TestHipNonbondedForce, TestHipVirtualSites.

Disassembly shows that the compiler splits branches of `if (skipBase+tgx < NUM_TILES_WITH_EXCLUSIONS)` and does
`SHFL(skipTiles, TILE_SIZE-1) < pos` checks in them separately, even though `__builtin_amdgcn_ds_bpermute`
is a convergent function. Apparently in this case not all lanes participate in each call.

* Simplify includeTile check using ballot

Handle relative include paths from force fields in data directories

* set box vectors of the inner contexts before atom reordering

* test for changing box vectors

* Optimized setPositions() and setVelocities()

* Fix test failures

* Improved residue indexing in error messages

* Fixed another one

* Fix GPU memory leak

* Undo CUDA change

Add new CHARMM and Amber force fields

* Use common API for kernels

* More code uses common interface

* Bug fixes

* Unified interface for sorting

* Simplified interface for FFT

* Use common event API for synchronization

* Minor changes to make code more consistent between platforms

* Common implementation of NonbondedForce

* Bug fixes

* Flag to enable list of single pairs

* CUDA and OpenCL use common implementation of NonbondedForce

* Fixed compilation error

* HIP uses common implementation of NonbondedForce

* Unified interface for queues

* Simplified stream handling in CudaFFT3D

* HIP implementation of ComputeQueue

* Created CustomVolumeForce

* Serialization for CustomVolumeForce

* Documentation for CustomVolumeForce

* Code simplification

* Removed unused code

* Added computeCurrentPressure() to MonteCarloBarostat

* Use instantaneous temperature to compute pressure

* Added computeCurrentPressure() to MonteCarloAnisotropicBarostat

* Added computeCurrentPressure() to MonteCarloMembraneBarostat

* Fixed compilation error

* Fixed error in typemap

* Added documentation on computing pressure

* Fixed CUDA compilation errors

* Made test case more robust

* Made a test case more robust

* Added computeCurrentPressure() to MonteCarloFlexibleBarostat

* Fixed compilation error

* More documentation on computing pressure

* Unified interface for FFTs

* AMOEBA uses unified interface for FFTs

* HIP implementation of common FFT interface

* Add correction for self energy of neutralizing plasma

* Fixed compilation errors

* Update total charge in copyParametersToContext()

* Bug fixes

* Fixed compilation errors in HIP

* Bug fix

* Use newer docker container for PPC

* Try different syntax

* Create bonds based on chem_comp_bond records

* Fixed a test that assumed bonds would be in a particular order

Check comment block length from DCD when appending

* Created DPDIntegrator class

* Reference implementation of DPDIntegrator

* Build neighbor list for DPDIntegrator

* Minor fixes

* Documentation for DPDIntegrator

* Python API for DPDIntegrator

* Preliminary OpenCL implementation of DPDIntegrator

* Enable USE_PERIODIC

* Use updated positions in DPD thermostat

* Working on neighbor list for OpenCL DPDIntegrator

* ReorderListener for particle types

* Serialization for DPDIntegrator

* CUDA implementation of DPDIntegrator

* HIP implementation of DPDIntegrator

* Fixed compile error in Python wrapper

* Fixed compile error in wrappers

* Fixed uninitialized memory in reference neighbor list

* Added DPDIntegrator to C++ API docs

* Fixed incorrect launch size

* Fixed nan in DPD random number generator

* Minor optimizations

* Improved load balancing

* Fixed an indexing error

* Neighbor list uses the maximum cutoff of any force

* Fixed HIP compilation error

* Fixed access to invalid memory

* Added test case for diffusion coefficient

* Try to debug segfaults on CI

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Debugging

* Possible fix

* Debugging

* Debugging

* Debugging

* Use correct block size on CPU OpenCL

* Workaround for bug in Intel's OpenCL for CPUs

* Removed an unnecessary define

* Removed debugging code

* Include Dart

* More Intel workarounds

* Workaround for error in NVIDIA OpenCL

* modifiy CMakeLists.txt to generate drude fortran wrapper

* modify doxyfile and wrapper generation wrapper

* add tests for correctness of step and time written in XTC and DCD

* improve tests

* improve xtc tests

* fix XTC/DCD time/step writing

* different approach by changing the reporters to not pass currentStep as firstStep but instead interval

* undo change

* Remove includes for Dart

* Fix CMake error

* Fixed broken link

* Pin to cmake<4.0

* Try to make the link checker stop complaining